Hmm. I got the impression that protoforms are factionless. In Beast Wars, the Predacons don't have any protoforms with them, so just end up stealing Maximal ones and over-writing their programming. At least in the case of Blackarachnia. Inferno is governed by his beast mode, and both the Fuzors are probably the closest we get to seeing new TF life emerge - they choose their allegiance based on what's in their nature.

In Animated, the Autobots guard the protoforms, but its never stated outright that they are Autobots - just innocents. The protoforms in Animated also seem to be sparkless (or it could be that they're blanks, like the one used in BW for Transmetal Optimus) and need to be infused with life from the Allspark. Possibly.